mutterer

/*
 * Making a pretty fluorogram
 * Olivier Burri, BioImaging & Optics Platform, EPFL
 */

run("Fluorescent Cells (400K)");

image = getTitle();
run("Split Channels");

mutterer

// This tool draws a line, and overlays its profile and some infos
 
 macro "Line and Profile Tool -C00bL1de0L1ee1" {
        getCursorLoc(x, y, z, flags);
        xstart = x; ystart = y;
        x2=x; y2=y;        
        while (true) {
            getCursorLoc(x, y, z, flags);
            if (flags&16==0) {
                dx=x2-xstart; dy=y2-ystart;

mutterer

// CZI batch project macro
// parses the file metadata to work around a bioformat bug
// that assigns wrong channel colors.
// edit the first two lines to use DIC in the projection or not
// and what projection mode is needed (see Image>stacks>Z project...)

useDic = true;
projectionMode = "Max Intensity";

var r,g,b;

mutterer

// creates series of montages
// use case: input stack of 200 images
// user wants 4x5 montage: 10 pages output.

source = getImageID;
slices=nSlices;
cols = 4;
rows = 5;
imagesPerPage = cols*rows;
for (i=0; i<slices/imagesPerPage; i++) {

mutterer

macro "MultiFreehand Tool - C00cT0f18M" {
  xs = newArray(1);
  ys = newArray(1);
  getCursorLoc(x, y, z, flags);
  xs[0]=x; ys[0]=y;
  lastx=x;lasty=y;
  leftclick=16;
  while (flags&leftclick>0) {
   getCursorLoc(x, y, z, flags);
   if ((x!=lastx)||(y!=lasty)) {

mutterer

// written at the request of S.Mingle.
// https://gist.github.com/mutterer/8fc04d0bdcc72a56072c

var baselineIndex=0;

macro "Help Action Tool - C00cT0f18?" {
  help = setup();
}

macro "Define BaseLine Action Tool - C00cT0f18BTaf18l" {

mutterer

/*
* By Olivier Burri, BioImaging & Optics Platform EPFL
* June 2016
* Provided as-is from a request on the ImageJ Forum
* http://forum.imagej.net/t/dividing-circle-into-8-equal-areas/1995
*/

var count = 0;  // Variable to know which circle we are working on

// If you install this macro, it will be mapped to the F2 Key

mutterer

// do auto contrast on all channels
// contrast is adjusted to min/max

import ij.*;

imp = IJ.getImage();
name = imp.getTitle();
print (name);
c = imp.getNChannels();

mutterer

s=getMetadata('info');
s = split(substring (s,indexOf(s,'>')+2));
for (i=0;i<nSlices;i++){
  setSlice(i+1);
  setMetadata("Label", (1*s[i]-1*s[0])/1000+" s");
}

mutterer

macro "move_overlay_elements Tool - C00cO11cc" {
	getCursorLoc(x, y, z, flags);
	while (flags&16>0) {
		getCursorLoc(x1, y1, z, flags);
		n = Overlay.size;
		for (i=0;i<n;i++) {
			Overlay.activateSelection(i);
			Roi.getBounds(rx, ry, width, height);
			Overlay.moveSelection(i, rx+x1-x, ry+y1-y);	
		}